I am sorry you are having problems with your system but let me help you.
As you say, when having RAID 1 configured the information should be exactly the same since it should be mirroring everything. It is very strange to see this happening.
I recommend you updating the BIOS and also you can try reinstalling the application. Here you can download it:
It turns out I don't think Matrix Storage Manager has been running all that time and I only just noticed I wasn't receiving it's notification on bootup. I don't know what stopped it running 6 months ago, or if that's the reason one drive was 6 months older than the other, but it's running again since I rebuilt the RAID, and I'm getting the "all's well" notification on boot, so I "assume" everything's back to normal. I'll just have to make sure I keep getting that notification, and pay closer attention to the BIOS screens on bootup.